[Resolved] Plug-in updates on WPML websites produce 404 errors through corrupt permalinks

On multilingual websites with WPML installed, updating other plugins causes an error 404 on all frontend pages. Refreshing the permalinks solves the issue.

Comparing the .htaccess file before and after the permalink refresh shows 2 differences in lines 3 and line 7:

### when the error 404 is present

RewriteEngine On
RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]
RewriteBase /fr/
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /fr/index.php [L]

### when the permalinks have been refreshed

RewriteEngine On
RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]

This problem is not specific to one website, and it is not a one-time issue either. This happend on half a dozen of my WPML websites on a regular basis over the last 12 months. And it does never happen with websites using Polylang or with single-language websites (around 50 websites in total).

My first approach was to find out if a specific plugin causes this issue. And for quite some time it seemed that Ninja Forms was the culprit. So I deactivated auto-updates for this plugin, and everything worked well for some months. But recently, updates of other plugins like Simple History, Yoast SEO, or Child Theme Configurator have triggered the same problem.

I even tried to implement an automatic permalink referesh after each plugin update through a custom function, but this was not reliable either.

So what could be the cause for this problem?